曲唇羊耳蒜叶绿体基因组密码子偏好性分析

Analysis of codon usage bias in the chloroplast genome of Liparis kumokiri

为了解兰科植物曲唇羊耳蒜叶绿体基因组密码子的使用偏好性及主要影响因素,从GenBank数据库下载曲唇羊耳蒜完整的叶绿体基因组序列并筛选得到51条符合分析要求的蛋白编码序列,利用CodonW软件和EMBOSS在线程序分析其密码子使用模式.结果显示:曲唇羊耳蒜叶绿体基因组密码子的第3位碱基多为A或T,GC_(3)仅为29%,远低于GC_(1)(46%)和GC_(2)(39%);有效密码子数(ENC)介于42~60之间,密码子偏好性较弱,ENC与GC_(3)呈极显著正相关.结合中性绘图、ENC-plot和PR2-plot分析,结果表明,曲唇羊耳蒜叶绿体基因组密码子使用偏好性主要受到自然选择压力的影响,突变压力的作用有限.同义密码子相对使用度(RSCU)数据分析共筛选出7个最优密码子,分别为UUG、CUU、UCA、ACA、AAU、AGA和GGA.对应性分析结果显示,曲唇羊耳蒜不同类型基因的密码子使用模式不同,其中光合系统基因具有相似的密码子使用模式,而其他类型基因的偏好性差异较大.

To understand the condon usage bias in the chloroplast genome of Liparis kumokiri and the main factors affecting the codon usage bias,the complete chloroplast sequence was downloaded from GenBank database,and 51 protein coding sequences were obtained after screening.CodonW software and EMBOSS online program were used to analyze its codon usage patterns.The results showed that the third codon positions of the chloroplast genome sequence of L.kumokiri are mostly A and T,and GC_(3) is only 29%,much lower than GC_(1)(46%)and GC_(2)(39%).The ENC value ranged from 42 to 60,which indicated that the codon usage bias was relatively low.There was an extremely significant positive correlation between ENC and GC_(3).Combining neutral plot,ENC-plot and PR2-plot analysis,the results showed that natural selection pressure was the dominant factor affecting the codon usage bias in the chloroplast genome of L.kumokiri,while the role of base mutation was extremely limited.The RSCU data analysis of synonymous codons identified a total of seven optimal codons,including UUG,CUU,UCA,ACA,AAU,AGA and GGA.The results of correspondence analysis showed that the codon usage patterns of different types of genes were different,in which photosynthetic system genes had similar codon usage bias,and other types of genes showed significant differences in bias.